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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN HISTONE-LYSINE N-METHYLTRANSFERASE SETMAR
 
Authors :  V. V. Lunin, H. Wu, H. Ren, E. Dobrovetsky, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, A. N. Plotnikov, Structural Geno Consortium (Sgc)
Date :  17 Dec 07  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Set Domain, Methyltransferase, Setmar, Chromatin Regulator, Dna Damage, Dna Repair, Dna-Binding, Nucleus, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, V. V. Lunin, H. Ren, E. Dobrovetsky, J. Weigelt, C. H. Arrowsmith A. M. Edwards, A. Bochkarev, J. Min, A. N. Plotnikov
The Crystal Structure Of Methyltransferase Domain Of Human Histone-Lysine N-Methyltransferase Setmar In Complex With Adohcy.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETMAR
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15B
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHISTONE-LYSINE N-METHYLTRANSFERASE DOMAIN: RESIDUES 2-290
    GeneSETMAR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:61 , CYS A:75 , CYS A:104 , CYS A:108BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS A:68 , CYS A:104 , CYS A:110 , CYS A:114BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWARECYS A:61 , CYS A:63 , CYS A:68 , CYS A:73BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWARECYS A:212 , CYS A:273 , CYS A:275 , CYS A:280BINDING SITE FOR RESIDUE ZN A 304
5AC5SOFTWARELYS A:135 , GLY A:136 , TRP A:137 , ASN A:177 , TYR A:178 , ARG A:206 , ASN A:209 , HIS A:210 , TYR A:248 , ARG A:263 , PRO A:272 , CYS A:273 , TYR A:274 , CYS A:275 , LEU A:284 , PHE A:286 , HOH A:427 , HOH A:473 , HOH A:515 , HOH A:524 , HOH A:627BINDING SITE FOR RESIDUE SAH A 305
6AC6SOFTWARECYS A:63 , VAL A:64 , LYS A:65 , THR A:66BINDING SITE FOR RESIDUE GOL A 306
7AC7SOFTWAREASN A:22 , LYS A:121 , GLN A:124 , HOH A:642BINDING SITE FOR RESIDUE GOL A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BO5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:28 -Pro A:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BO5)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRE_SETPS50867 Pre-SET domain profile.SETMR_HUMAN73-136  1A:59-122
2SETPS50280 SET domain profile.SETMR_HUMAN139-263  1A:125-249
3POST_SETPS50868 Post-SET domain profile.SETMR_HUMAN283-299  1A:269-285

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003580651aENSE00001498847chr3:4344988-4345210223SETMR_HUMAN1-52521A:11-3828
1.3cENST000003580653cENSE00001733551chr3:4354582-4355445864SETMR_HUMAN53-3402881A:39-289 (gaps)251
1.4eENST000003580654eENSE00001821318chr3:4357896-43592511356SETMR_HUMAN341-6843440--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:269
 aligned with SETMR_HUMAN | Q53H47 from UniProtKB/Swiss-Prot  Length:684

    Alignment length:279
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294         
          SETMR_HUMAN    25 TEQLDVACGQENLPVGAWPPGAAPAPFQYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRDIGSGGKYAEPVFECNVLCRCSDHCRNRVVQKGLQFHFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREHVYNGQVMETFVDPTYIGNIGRFLNHSCEPNLLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSEDKERLDHGKLRKPCYCGAKSCTAFLPFDSS 303
               SCOP domains d3bo5a_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3bo5A00 A:11-289 SET domain                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee.........ee....ee...........................hhhhh.............-----.....ee...............hhhhh....eeeee.....eeeee........eeee..eeeehhhhhhhhhh..........eeeee.-----.eeeeeeeeeee.hhhhhee.....eeeeeee......eeeeee........eeee............eeeeeee.....................ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------PRE_SET  PDB: A:59-122 UniProt: 73-136                          --SET  PDB: A:125-249 UniProt: 139-263                                                                                         -------------------POST_SET         ---- PROSITE
               Transcript 1 Exon 1.1a  PDB: A:11-38     Exon 1.3c  PDB: A:39-289 (gaps) UniProt: 53-340 [INCOMPLETE]                                                                                                                                                                                                Transcript 1
                 3bo5 A  11 TEQLDVACGQENLPVGAWPPGAAPAPFQYTPDHVVGPGADIDPTQITFPGCICVKTPCLPGTCSCLRHGENYDDNSCLRD-----KYAEPVFECNVLCRCSDHCRNRVVQKGLQFHFQVFKTHKKGWGLRTLEFIPKGRFVCEYAGEVLGFSEVQRRIHLQTKSDSNYIIAIREH-----VMETFVDPTYIGNIGRFLNHSCEPNLLMIPVRIDSMVPKLALFAAKDIVPEEELSYDYSGRYLNLTVSASKERLDHGKLRKPCYCGAKSCTAFLPFDSS 289
                                    20        30        40        50        60        70        80        90     | 100       110       120       130       140       150       160       170       180    |    -|      200       210       220       230       240       250       260       270       280         
                                                                                                          90    96                                                                                      185   191                                                                                                  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BO5)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SETMR_HUMAN | Q53H47)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0044547    DNA topoisomerase binding    Interacting selectively and non-covalently with a DNA topoisomerase.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046975    histone methyltransferase activity (H3-K36 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 of the histone H3 protein.
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0000014    single-stranded DNA endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0000737    DNA catabolic process, endonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    GO:0000729    DNA double-strand break processing    The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0097676    histone H3-K36 dimethylation    The modification of histone H3 by addition of two methyl groups to lysine at position 36 of the histone.
    GO:0010452    histone H3-K36 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone.
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0044774    mitotic DNA integrity checkpoint    A mitotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction.
    GO:0071157    negative regulation of cell cycle arrest    Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:2001251    negative regulation of chromosome organization    Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:2000373    positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity    Any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.
    GO:2001034    positive regulation of double-strand break repair via nonhomologous end joining    Any process that activates or increases the frequency, rate or extent of double-strand break repair via nonhomologous end joining.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SETMR_HUMAN | Q53H473f2k 3k9j 3k9k

(-) Related Entries Specified in the PDB File

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